DNA methylation is central to such diverse phenomena as restriction and modification in bacteria, repeat induced point-mutation in fungi, and for programming gene expression patterns, embryonic development, and DNA replication in vertebrates. Our long term goal is to understand from a structural standpoint how different classes of DNA methyltransferases work, with specific emphasis on the mechanism of base flipping. The starting point for most of these studies is the structures of the Hhal methyltransferase (a C5-cytosine methyltransfrase) in binary complex with S-adenosyl-L-methionine and in ternary complex with DNA and S-adenosyl-L- homocysteine. The structures of Hhal methyltransfrase demonstrate a remarkable novel solution to the difficult problem of reaching a target base buried in the double helix: rotation of a DNA nucleotide out of' -the double helix and into the protein binding pocket ('base flipping'). This base flipping mechanism is not unique to DNA methyltransferases, but appears to be widely used in other DNA modification processes such as DNA repair and DNA ligation. The structures also reveal other common properties of the family of DNA methyltransferases: nearly complete separation of sequence recognition and catalysis into two structural domains and nearly identical structure of the sequence-recognition loops despite complete divergence of DNA substrate sequence. Our immediate goals are to dissect the mechanism of base flipping and the catalysis of C5-cytosine methylation by structural studies with mismatched bases, cytosine analogs, or mutant M.Hhal proteins defective at some point in the reaction pathway, and to demonstrate more examples of base flipping and to study the catalytic mechanism of DNA amino-methyltransferases by determining the structures of Pvull N4-cytosine methyltransferase and T4 Dam (DNA adenine methyltransferase) in complex with DNA.